diff --git a/recipes/hmftools-chord/meta.yaml b/recipes/hmftools-chord/meta.yaml
index 3634b0ab4f329..c529dd49582ae 100644
--- a/recipes/hmftools-chord/meta.yaml
+++ b/recipes/hmftools-chord/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "2.1.0_beta" %}
-{% set beta_suffix = ".1" %}
-{% set sha256 = "25a4dfd8a0ab436e0f23d94e77cebb59a0830a052a90c823844b798bd409bfc3" %}
+{% set beta_suffix = ".2" %}
+{% set sha256 = "847e0239b7440b70d67957d38afb3ab42bd3acecb931afc49ab8aef4c248a1da" %}
 
 package:
   name: hmftools-chord
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 2
+  number: 3
   run_exports:
     - {{ pin_subpackage("hmftools-chord", max_pin="x.x") }}
 
diff --git a/recipes/hmftools-cuppa/build.sh b/recipes/hmftools-cuppa/build.sh
index 0cd12bf1a92f0..b2466610649c4 100644
--- a/recipes/hmftools-cuppa/build.sh
+++ b/recipes/hmftools-cuppa/build.sh
@@ -1,12 +1,17 @@
 #!/bin/bash
 
 TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
-[ -d "$TGT" ] || mkdir -p $TGT/{,chart/}
+[ -d "$TGT" ] || mkdir -p $TGT
 [ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
 
 cd "${SRC_DIR}"
-mv jar/cuppa*.jar $TGT/cuppa.jar
-${PYTHON} -m pip install --no-build-isolation --no-deps --no-cache-dir -vvv src/cuppa/src/main/python/pycuppa/
+mv cuppa*.jar $TGT/cuppa.jar
 
 cp $RECIPE_DIR/cuppa.sh $TGT/cuppa
 ln -s $TGT/cuppa ${PREFIX}/bin/
+chmod 0755 "${PREFIX}/bin/cuppa"
+
+mkdir -p /tmp/cuppa_jar/
+unzip -n $TGT/cuppa.jar -d /tmp/cuppa_jar/
+${PYTHON} -m pip install --no-build-isolation --no-deps --no-cache-dir -vvv /tmp/cuppa_jar/pycuppa/
+rm -r /tmp/cuppa_jar/
diff --git a/recipes/hmftools-cuppa/meta.yaml b/recipes/hmftools-cuppa/meta.yaml
index 840622e449152..bb1424cfae91d 100644
--- a/recipes/hmftools-cuppa/meta.yaml
+++ b/recipes/hmftools-cuppa/meta.yaml
@@ -1,22 +1,18 @@
 {% set version = "2.3.0_beta" %}
-{% set sha256_jar = "69f94a54f232a2a22927dce165120d1f166d4931bfb8f299515edaa577607c7c" %}
-{% set sha256_src = "65a2070e78243fed975b8738d2ce79dfead1a5702c2bc91e26488c806e25d158" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "ae3a3d9bc31e45cba52943df01b6f8f190beff904dff392e6413c1396d7db36d" %}
 
 package:
   name: hmftools-cuppa
   version: '{{ version }}'
 
 source:
-  - folder: jar
-    url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa-{{ version|replace(".0", "") }}.jar
-    sha256: '{{ sha256_jar }}'
-  - folder: src
-    url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/cuppa-v{{ version }}.tar.gz
-    sha256: '{{ sha256_src }}'
+  url: https://github.com/hartwigmedical/hmftools/releases/download/cuppa-v{{ version }}/cuppa_v{{ version|replace(".0", "") }}{{ beta_suffix }}.jar
+  sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("hmftools-cuppa", max_pin="x.x") }}
 
@@ -24,6 +20,7 @@ requirements:
   host:
     - python ==3.11
     - r-base >=4.2,<4.3.0a0
+    - unzip
   run:
     - openjdk >=8
     - python ==3.11